X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FAlignFile.java;h=a800f0652d6b73e5273369cd5d2164817ebe38b3;hb=a1146b0c16d1bf25d0174031a4812e4ea6021c22;hp=04ddff3fe9599a277032650e50a69df81312db6c;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 04ddff3..a800f06 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -1,6 +1,6 @@
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
@@ -25,33 +25,37 @@ import java.io.*;
 import java.util.*;
 
 
-public abstract class AlignFile extends FileParse {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public abstract class AlignFile extends FileParse
+{
     int noSeqs = 0;
     int maxLength = 0;
     Vector seqs;
-    Vector headers;
+    Vector annotations;
     long start;
     long end;
+    boolean jvSuffix = true;
 
-    public AlignFile() {
+    /**
+     * Creates a new AlignFile object.
+     */
+    public AlignFile()
+    {
     }
 
-    public AlignFile(String inStr) {
-        initData();
-        System.out.println("is this ever called??");
-
-        try {
-            parse();
-        } catch (Exception ex) {
-        }
-    }
 
     /**
      * Constructor which parses the data from a file of some specified type.
      * @param inFile Filename to read from.
      * @param type   What type of file to read from (File, URL)
      */
-    public AlignFile(String inFile, String type) throws IOException {
+    public AlignFile(String inFile, String type) throws IOException
+    {
         super(inFile, type);
 
         initData();
@@ -62,50 +66,76 @@ public abstract class AlignFile extends FileParse {
     /**
      * Return the seqs Vector
      */
-    public Vector getSeqs() {
+    public Vector getSeqs()
+    {
         return seqs;
     }
 
     /**
      * Return the Sequences in the seqs Vector as an array of Sequences
      */
-    public SequenceI[] getSeqsAsArray() {
+    public SequenceI[] getSeqsAsArray()
+    {
         SequenceI[] s = new SequenceI[seqs.size()];
 
-        for (int i = 0; i < seqs.size(); i++) {
+        for (int i = 0; i < seqs.size(); i++)
+        {
             s[i] = (SequenceI) seqs.elementAt(i);
         }
 
         return s;
     }
 
+    public void addAnnotations(Alignment al)
+    {
+      for(int i=0; i<annotations.size(); i++)
+      {
+        al.addAnnotation(
+            (AlignmentAnnotation)annotations.elementAt(i)
+            );
+      }
+
+    }
+
     /**
      * Initialise objects to store sequence data in.
      */
-    protected void initData() {
+    protected void initData()
+    {
         seqs = new Vector();
-        headers = new Vector();
+        annotations = new Vector();
     }
 
-    protected void setSeqs(SequenceI[] s) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     */
+    protected void setSeqs(SequenceI[] s)
+    {
         seqs = new Vector();
 
-        for (int i = 0; i < s.length; i++) {
+        for (int i = 0; i < s.length; i++)
+        {
             seqs.addElement(s[i]);
         }
     }
 
     // Checks whether sequence is valid aa characters
-    protected boolean isValidProteinSequence(String sequence) {
-        for (int i = 0; i < sequence.length(); i++)
-            if (!jalview.schemes.ResidueProperties.aaHash.containsKey(
-                        String.valueOf(sequence.charAt(i)))) {
+    protected boolean isValidProteinSequence(char [] sequence)
+    {
+        for (int i = 0; i < sequence.length; i++)
+            if (jalview.schemes.ResidueProperties.aaIndex[sequence[i]]==-1)
+            {
+                invalidCharacter = sequence[i];
                 return false;
             }
 
         return true;
     }
 
+    char invalidCharacter;
+
     /**
      * This method must be implemented to parse the contents of the file.
      */
@@ -115,4 +145,45 @@ public abstract class AlignFile extends FileParse {
      * Print out in alignment file format the Sequences in the seqs Vector.
      */
     public abstract String print();
+
+    public void addJVSuffix(boolean b)
+    {
+      jvSuffix = b;
+    }
+
+    /**
+     * A general parser for ids.
+     *
+     * @String id Id to be parsed
+     */
+    Sequence parseId(String id)
+    {
+      Sequence seq = null;
+      id = id.trim();
+      int space = id.indexOf(" ");
+      if(space>-1)
+      {
+        seq = new Sequence(id.substring(0, space),"");
+        seq.setDescription(id.substring(space+1));
+      }
+      else
+      {
+        seq = new Sequence(id, "");
+      }
+
+      return seq;
+    }
+
+    /**
+     * Creates the output id.
+     * Adds prefix Uniprot format source|id
+     * And suffix Jalview /start-end
+     *
+     * @String id Id to be parsed
+     */
+    String printId(SequenceI seq)
+    {
+     return seq.getDisplayId(jvSuffix);
+    }
+
 }